Bismark report for: ../../data/raw-wgbs/270M_1.fastq.gz and ../../data/raw-wgbs/270M_2.fastq.gz (version: v0.24.2)
Bismark was run with Bowtie 2 against the bisulfite genome of /mmfs1/gscratch/scrubbed/sr320/github/project-mytilus-methylation/output/01-bismark-init/ with the specified options: -q --score-min L,0,-0.6 -p 30 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
Option '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB)

Final Alignment report
======================
Sequence pairs analysed in total:	10000
Number of paired-end alignments with a unique best hit:	4693
Mapping efficiency:	46.9% 
Sequence pairs with no alignments under any condition:	3968
Sequence pairs did not map uniquely:	1339
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	2328	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	1	(complementary to (converted) bottom strand)
CT/GA/GA:	2364	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	222619

Total methylated C's in CpG context:	3502
Total methylated C's in CHG context:	1006
Total methylated C's in CHH context:	5216
Total methylated C's in Unknown context:	276

Total unmethylated C's in CpG context:	23169
Total unmethylated C's in CHG context:	35155
Total unmethylated C's in CHH context:	154571
Total unmethylated C's in Unknown context:	1026

C methylated in CpG context:	13.1%
C methylated in CHG context:	2.8%
C methylated in CHH context:	3.3%
C methylated in Unknown context (CN or CHN):	21.2%


Bismark completed in 0d 0h 0m 23s